Video Editing Workflow: Use a separate scene for VSE?
Let me explain you a workflow for video editing based on my experience. As every aspect of 3d, everybody has their methods, but the following has worked pretty well for me after trying out a lot of different workflows.

(First of all do not "render" (from actually 3d scenes) from the VSE,  unless you are doing animatics, layout or something that are not final renders)


Start off by rendering your three scenes into single image sequences
without any compositing and organized into separate folders (OpenEXR
is a recommended format).
Do the compositing using your image sequences and render (again) into single image sequences.
Then, using a new blender scene, render the sequences into single movie files.
In your case you should have three movie files to do the final
editing in a blender file used only for editing.


Render image sequences > Compositing image sequences > Movie files > Editing has given me great results. Using image sequences lets you fixed any problems in the renders without rendering the whole thing again, and editing with movie files will let you have a waaay faster playback and editing.

Now, be careful with resolution, FPS and other settings. Every new scene that you use will overwrite the settings. So you have to be very organized in that matter. I recommend you to establish some settings before working on your project. Preferably all your scenes must have the same resolution, or you'll have some weirdly scaled result.